diff --git a/changelog/fragments/1764873750-Merge-multiple-agent-keys-when-loading-config.yaml b/changelog/fragments/1764873750-Merge-multiple-agent-keys-when-loading-config.yaml
new file mode 100644
index 00000000000..68b5335f7f1
--- /dev/null
+++ b/changelog/fragments/1764873750-Merge-multiple-agent-keys-when-loading-config.yaml
@@ -0,0 +1,32 @@
+# Kind can be one of:
+# - breaking-change: a change to previously-documented behavior
+# - deprecation: functionality that is being removed in a later release
+# - bug-fix: fixes a problem in a previous version
+# - enhancement: extends functionality but does not break or fix existing behavior
+# - feature: new functionality
+# - known-issue: problems that we are aware of in a given version
+# - security: impacts on the security of a product or a user’s deployment.
+# - upgrade: important information for someone upgrading from a prior version
+# - other: does not fit into any of the other categories
+kind: bug-fix
+
+# Change summary; a 80ish characters long description of the change.
+summary: Merge multiple agent keys when loading config
+
+# Long description; in case the summary is not enough to describe the change
+# this field accommodate a description without length limits.
+# NOTE: This field will be rendered only for breaking-change and known-issue kinds at the moment.
+#description:
+
+# Affected component; usually one of "elastic-agent", "fleet-server", "filebeat", "metricbeat", "auditbeat", "all", etc.
+component: elastic-agent
+
+# PR URL; optional; the PR number that added the changeset.
+# If not present is automatically filled by the tooling finding the PR where this changelog fragment has been added.
+# NOTE: the tooling supports backports, so it's able to fill the original PR number instead of the backport PR number.
+# Please provide it if you are adding a fragment for a different PR.
+#pr: https://github.com/owner/repo/1234
+
+# Issue URL; optional; the GitHub issue related to this changeset (either closes or is part of).
+# If not present is automatically filled by the tooling with the issue linked to the PR number.
+issue: https://github.com/elastic/elastic-agent/issues/3717
diff --git a/internal/pkg/agent/cmd/run_test.go b/internal/pkg/agent/cmd/run_test.go
index f2782866cd0..a1f3bc296e2 100644
--- a/internal/pkg/agent/cmd/run_test.go
+++ b/internal/pkg/agent/cmd/run_test.go
@@ -5,14 +5,29 @@
 package cmd
 
 import (
+	_ "embed"
 	"fmt"
+	"os"
+	"path/filepath"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
 
+	"github.com/elastic/elastic-agent-libs/logp"
+	"github.com/elastic/elastic-agent/internal/pkg/agent/application/paths"
+	"github.com/elastic/elastic-agent/internal/pkg/agent/configuration"
 	monitoringCfg "github.com/elastic/elastic-agent/internal/pkg/core/monitoring/config"
 )
 
+var (
+	//go:embed testdata/run/singlelogging.yaml
+	singleLoggingConfig []byte
+
+	//go:embed testdata/run/splitlogging.yaml
+	splitLoggingConfig []byte
+)
+
 func Test_initTracer(t *testing.T) {
 	tenPercentSamplingRate := float32(0.1)
 
@@ -93,3 +108,49 @@ func Test_initTracer(t *testing.T) {
 		})
 	}
 }
+
+func TestRunLoadConfig(t *testing.T) {
+	tests := []struct {
+		name   string
+		file   []byte
+		expect func() *configuration.Configuration
+	}{{
+		name: "single logging entry",
+		file: singleLoggingConfig,
+		expect: func() *configuration.Configuration {
+			cfg := configuration.DefaultConfiguration()
+			cfg.Settings.LoggingConfig.Level = logp.DebugLevel
+			cfg.Settings.LoggingConfig.ToFiles = true
+			cfg.Settings.LoggingConfig.ToStderr = false
+
+			return cfg
+		},
+	}, {
+		name: "split logging entries",
+		file: splitLoggingConfig,
+		expect: func() *configuration.Configuration {
+			cfg := configuration.DefaultConfiguration()
+			cfg.Settings.LoggingConfig.Level = logp.DebugLevel
+			cfg.Settings.LoggingConfig.ToFiles = true
+			cfg.Settings.LoggingConfig.ToStderr = false
+
+			return cfg
+		},
+	}}
+
+	origCfgDir := paths.Config()
+	t.Cleanup(func() { paths.SetConfig(origCfgDir) })
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			paths.SetConfig(dir)
+			err := os.WriteFile(filepath.Join(dir, paths.DefaultConfigName), tt.file, 0o644)
+			require.NoError(t, err)
+
+			cfg, err := loadConfig(t.Context(), nil)
+			require.NoError(t, err)
+			require.Equal(t, tt.expect(), cfg)
+		})
+	}
+}
diff --git a/internal/pkg/agent/cmd/testdata/run/singlelogging.yaml b/internal/pkg/agent/cmd/testdata/run/singlelogging.yaml
new file mode 100644
index 00000000000..1165f8b5553
--- /dev/null
+++ b/internal/pkg/agent/cmd/testdata/run/singlelogging.yaml
@@ -0,0 +1,5 @@
+agent:
+  logging:
+    level: debug
+    to_files: true
+    to_stderr: false
diff --git a/internal/pkg/agent/cmd/testdata/run/splitlogging.yaml b/internal/pkg/agent/cmd/testdata/run/splitlogging.yaml
new file mode 100644
index 00000000000..8cf89a26780
--- /dev/null
+++ b/internal/pkg/agent/cmd/testdata/run/splitlogging.yaml
@@ -0,0 +1,5 @@
+agent.logging.level: debug
+agent.logging.to_files: true
+agent:
+  logging:
+    to_stderr: false
diff --git a/internal/pkg/config/config.go b/internal/pkg/config/config.go
index 457d66bebaa..a416f5819e7 100644
--- a/internal/pkg/config/config.go
+++ b/internal/pkg/config/config.go
@@ -56,6 +56,7 @@ var DefaultOptions = []interface{}{
 	ucfg.IgnoreCommas,
 	ucfg.ResolveEnv,
 	ucfg.VarExp,
+	ucfg.FieldMergeValues("agent"),
 	VarSkipKeys("inputs", "outputs"),
 	OTelKeys("connectors", "receivers", "processors", "exporters", "extensions", "service"),
 }